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v92.0 (released) snovault 1.0.37

  1. ENCD-4924 fix bugs in moving controls (#3001)
  2. ENCD-4928-run-npm-once (#3002)
  3. ENCD-4925-increase-circle-es-heap (#2999)
  4. ENCD-4895-adjust-long-read-RNA-audit (#2982)
  5. ENCD-4920-update-snovault-1.0.37 (#2997)
  6. ENCD-3336-Upgrade-postgres-11 (#2976)
  7. ENCD-4892 region search refresh (#2978)
  8. ENCD-4861 add enum to user groups(#2964)
  9. ENCD-4849-fix-description-misalignment-in-docs (#2958)
  10. ENCD-4840-Add-Donor-accession-boost-value (#2975)
  11. ENCD-4674 move Control from Target to Experiment (#2866)
  12. ENCD-4894 Exclude long read RNA-seq from RNA fragment size audit and add tests for missing read_length (#2969)
  13. ENCD-4900 Add status check for matching md5 sum audit (#2972)
  14. ENCD-4903-image-update (#2983)
  15. [HOTFIX] SNO-120-stream-large-json (#2980)
  16. ENCD-4885 add entry for functional characterization assays (#2981)
  17. ENCD-4916-fix-circleci (#2986)
  18. ENCD-4816 Summary release date source change (#2961)
  19. ENCD-4722 install Valis as component (#2937)
  20. ENCD-4855 Extra-wide search facets (#2948)
  21. ENCD-4876-add-assembly-annotations (#2956)
  22. ENCD-4865 remove fcc assay term names from experiements (#2952)
  23. SNO-115-delete-old-search-code (#2966)
  24. ENCD-4731 Add audits for experiment series (#2960)
  25. ENCD-4890-library-target-size-range (#2970)
  26. ENCD-4901-redirect-file-downloads (#2968)
  27. ENCD-4902-fix-graph-x-tick (#2971)
  28. ENCD-4887-fix-audit-detail-bugs (#2957)
  29. ENCD-4862-fix-audit-script error (#2962)
  30. ENCD-4836-bring-back-alt-color-report-view-table (#2963)
  31. ENCD-4854 Change severity of missing controlled by audit (#2953)
  32. ENCD-4858-table-border (#2949)
  33. ENCD-4863-audit-paths (#2940)
  34. ENCD-4866 fix sorttable comment (#2947)
  35. ENCD-4868-update-organ-slims (#2954)
  36. ENCD-4888-add-admin-access-key-to-insert (#2946)
  37. ENCD-4079-fix-npm-audit-errors (#2913)
  38. ENCD-4816 Summary release date source change (#2961)

v91.0 (released) snovault 1.0.36

  1. ENCD-4891-region-search-crash-with-position (#2955)
  2. ENCD-4878-update-robots-txt (#2939)
  3. ENCD-4884-allow-apache-conf-variables-on-deploy
  4. ENCD-4718-Refactor-deployment-based-on-build-type
  5. ENCD-4881-fix-NTR-audit-detail (#2943)
  6. ENCD-4879-workaround-for-improper-date (#2942)
  7. ENCD-4880-restore-disabled-buttons (#2941)
  8. ENCD-4875-update-snovault-1.0.36 (#2936)
  9. ENCD-4803-new-search-views (#2928)
  10. ENCD-4871-summary-dates (#2935)
  11. ENCD-4398-allow-unprivileged-login-for-cart(#2869)
  12. ENCD-4753-fix-audit-details-and-cleanup (#2927)
  13. ENCD-4838 Remove Experiment Classification from Experiment Schema (#2929)
  14. ENCD-4856 break up test suite for circle-ci (#2932)
  15. ENCD-4826 updated chip-seq qc (#2930)
  16. ENCD-4846 Fix microRNA raw data table headers (#2933)
  17. ENCD-4820-update-ontology (#2917)
  18. ENCD-4690-remove-cln-msg-in-file-assoc-graph (#2903)
  19. ENCD-4050-replace-momentjs (#2914)
  20. ENCD-4832 remove border on empty results (#2926)
  21. ENCD-4844-Add-Jessica-to-users
  22. ENCD-4837 assay title facet for experimental series (#2921)
  23. ENCD-4213-replace-cookie-monster (#2906)

v90.0 (released) snovault 1.0.34

  1. ENCD-4828 Remove extra div and style .box.facets (#2919)
  2. ENCD-4827 Restore old link underlines (#2918)
  3. ENCD-4824 Make Safari search box styling the same as others (#2915)
  4. ENCD-4825 Return button style and clean up CSS (#2916)
  5. ENCD-4817 Fix default value (#2902)
  6. ENCD-4538 Fixed minor typos and formatting inconsistencies (#2895)
  7. ENCD-4376 new ATAC-seq QC (#2907)
  8. ENCD-4819 Use not-allowed cursor on disabled inputs, buttons (#2909)
  9. ENCD-4818 downgrade ChIP-seq QM schema versions (#2908)
  10. ENCD-4788-add-mg-kg-treat (#2900)
  11. ENCD-4714-move-pg-deploy-echos-to-file (#2905)
  12. ENCD-4794 update bulk RNA QC (#2901)
  13. ENCD-4680 Remove and replace Bootstrap styling (#2894)
  14. ENCD-4783-set-iam-role-on-deploy (#2904)
  15. ENCD-4797 Add new file FCC output_type elements reference (#2899)
  16. ENCD-4789 Add wranglers' uuids to antibody_characterization.json (#2898)
  17. ENCD-4776 Add Bonita's info to user.json (#2897)
  18. ENCD-4800 Fix Chrome slow scrolling with scrollable facets (#2892)

v89.0 (released) snovault 1.0.34

  1. ENCD-4811 Change breadcrumb pluralization (#2893)
  2. ENCD-4801 fix bugs related to award embedding in AntibodyLot (#2890)
  3. ENCD-4539-pipelines-missing-alt-accession (#2879)
  4. ENCD-4802 update ChIP-seq QMs (#2891)
  5. ENCD-4641 new ChIP-seq quality metrics (#2789)
  6. ENCD-4779 fix default tracks (#2884)
  7. ENCD-4664 FCC experiment modeling (#2882)
  8. ENCD-4768 Add matching md5sum property (#2870)
  9. ENCD-4769 Add dataset properties on ExperimentPage (#2888)
  10. ENCD-4711-update-sn-atac-name (#2889)
  11. ENCD-4785 correcting md5 uniqueness behavior (#2881)
  12. ENCD-4778 Add link for Mouse Dev Series collection to drop down menu (#2874)
  13. ENCD-4775 default to mm10 over mm9 (#2883)
  14. ENCD-4773 fix browser styles on IE 11 (#2872)
  15. ENCD-4750 rename duplicated health status column (#2876)
  16. ENCD-4791 remove Quick View (#2886)
  17. ENCD-4745 biosample characterization audit update (#2880)
  18. ENCD-4730-change-menu-item-names-for-matrices (#2877)
  19. ENCD-4740-fix-broken-report-link (#2862)
  20. ENCD-4729-fix-add-minus-btn-on-graph (#2885)
  21. ENCD-4228-genetic-mod-missing-alter-acc (#2878)
  22. ENCD-4752 read_structure for fastq files (#2868)
  23. ENCD-4646-add-search-btn-top-nav (#2871)
  24. ENCD-4608 ENCODE4 antibody review (#2849)
  25. ENCD-4744 Added erez-aiden to aliases list (#2873)

v88.0 (released) snovault 1.0.34

  1. ENCD-4761 Fix table display for non-anno and exp pages (#2861)
  2. ENCD-4762 make-search-fields-consistent (#2860)
  3. ENCD-3904 remove-quotation-marks (#2850)
  4. ENCD-4715 Integrate Valis browser (#2809)
  5. ENCD-4760 Update to snovault 1.0.34 (#2858)
  6. SNO-108 improve-search-new (#2856)
  7. ENCD-4724 md5 uniqueness adjustment (#2855)
  8. ENCD-4720 change-es-deploy-arg-to-bool (#2853)
  9. ENCD-4692 Add mechanism for audit details to include links (#2854)
  10. SNO-106 fix-spec-char-500-error (#2851)
  11. ENCD-4685 matrix-vertical-scroll (#2836)
  12. ENCD-4717 adding output types (#2839)
  13. ENCD-4682 Award title required (#2831)
  14. ENCD-4677 Update biosample characterization audit (#2847)
  15. ENCD-3567 Upgrade React JS 15.6.0 (#2841)
  16. ENCD-4697 add biosample summary to experiment series (#2842)
  17. ENCD-4701 Update STAR quality metric for chimeric reads (#2843)
  18. ENCD-4706 store-circleci-results (#2848)
  19. ENCD-4702 remove-dup-gm-column-in-biosample (#2846)
  20. ENCD-4684 remove-facet-duplication (#2844)
  21. ENCD-4511 make-pool-table (#2820)
  22. ENCD-4699 Fix Javascript crash display series file tables (#2829)
  23. ENCD-4063 ambulance-icon-for-only-logged-in-users (#2819)
  24. SNO-105 fix-batchupgrade-tests-sno103 (#211)
  25. ENCD-4772 Fix context usage with GM object pages (#2865)
  26. ENCD-4771 gene locations for mouse incorrectly padded (#2864)
  27. ENCD-4770 Only filter revoked files when needed (#2863)

v87.0 (released) snovault 1.0.32/1.0.33

  1. ENCD-4723 update-snovault-1.0.33 (#2840)
  2. ENCD-4716 Update cloud init deployment (#2830)
  3. ENCD-4713 manually-install-oracle-java-11 (#2830)
  4. ENCD-4719 Use 16 processes demo batchupgrade (#2830)
  5. ENCD-4665 organize-cluster-cloud-yamls (#2830)
  6. ENCD-4688 remove-unused-code-from-deploy (#2830)
  7. ENCD-4704 Fix frozen column for Safari (#2825)
  8. ENCD-4708 Fix the target column on experiment series page (#2828)
  9. SNO-102 use-openjdk-java-for-circleci (#2832)
  10. ENCD-4703 test-submitter-user-circleci-fix (#2824)
  11. ENCD-4654 change ChIP-seq to TF ChIP-seq (#2806)
  12. ENCD-4698 update-snovault-1.0.32 (#2822)
  13. ENCD-4662 Experiment series (#2812)
  14. ENCD-4659 batch-download-unit-test (#2815)
  15. ENCD-4514 add MouseDevSeries internal tag (#2821)
  16. ENCD-4106 Remove kyoto from aliases and dbxrefs (#2803)
  17. ENCD-4672 Remove news page and instead link to generic search (#2811)
  18. ENCD-4653 add AWS link (#2798)
  19. ENCD-4415 Add GM perturbation property (#2816)
  20. ENCD-4694 restrict use of FCC in experiments (#2817)
  21. ENCD-4471 add-prod-id-source-treatment (#2808)
  22. ENCD-4671 port tests circleci (#2810)
  23. ENCD-4062 Fix read name details dependency (#2797)
  24. ENCD-4613 Changed cRE to cCRE with batch upgrades and tests (#2763)
  25. ENCD-4656 Fix BDD Travis CI test failures (#2793)
  26. ENCD-4651 add new analysis step type (#2785)
  27. ENCD-4586 Freeze left column of matrix (#2799)
  28. SNO-100 Parallelize batchupgrade script
  29. SNO-92 fix-batch-upgrade-logging
  30. SNO-101 Refactor batchupgrade

v86.0 (released) snovault 1.0.31

  1. ENCD-4676 add-nagios-role-deployment (#2796)
  2. ENCD-4666 update-snovault-1.0.31 (#2790)
  3. ENCD-4657 add-s3-uri-to-metadata (#2786)
  4. ENCD-4639 Organize demo cloud yaml (#2773)
  5. ENCD-4634 Add database to file_format (#2770)
  6. ENCD-4541 Add multiple facets to cart view pages (#2780)
  7. ENCD-4633 Update saucelabs connect version 4.5.3 (#2788)
  8. ENCD-4609 Exclude fccs institutional certification (#2764)
  9. ENCD-4631 add new qc object for gencode categories (#2787)
  10. ENCD-4492 audit-to-chk-fq-non-fq-pair (#2776)
  11. ENCD-4084 date selector facet (#2759)
  12. ENCD-4600 Add MIME type for ab1 attachment (#2774)
  13. SNO-93 user-count-does-not-match (#2758)
  14. ENCD-4647 Display QC metric properties with multitype (#2783)
  15. SNO-90 added-advanced-search (#2729)
  16. ENCD-4648 always-show-cloud-metadata (#2777)
  17. ENCD-4642 Stop home banner truncation (#2781)
  18. ENCD-4599 fix audit detail typo (#2765)
  19. ENCD-4400 added-creative-commons-logo (#2750)
  20. ENCD-4611 update 2 polyA assay_titles (#2761)

v85.2 (unreleased) snovault 1.0.30

  1. ENCD-4650 update-snovault-1.0.30 (#2778)
  2. ENCD-4620 indexing-failures (#2775)

v85.1 (released)

  1. ENCD-4628 Add a mechanism for a home page banner (#2768)

v85.0 (released) snovault 1.0.29

  1. ENCD-4625 Fix target upgrade for chromatin remodeler (#2755)
  2. ENCD-4624 update-snovault-1.0.29 (#2754)
  3. ENCD-4392 update-to-java-11 (#2726)
  4. SNO-91 update-java-ref (#2753)
  5. SNO-87 fix-profile-trailing-slash (#2710)
  6. ENCD-4619 Add experiment classification to data insert (#2752)
  7. ENCD-4361 validate-schema-set-status (#2748)
  8. ENCD-4558 add 2 new FCC assays
  9. ENCD-4563 shorten 3 assay titles
  10. ENCD-4579 update to EFO3 and update ontology.json and docs
  11. ENCD-4536 long read RNA audit (#2735)
  12. ENCD-4535 long rna qc (#2673)
  13. SNO-86 escape-search-text (#2709)
  14. ENCD-3642 fix-file-format-download (#2746)
  15. ENCD-4602 Update link on home page button (#2744)
  16. ENCD-4606 Add error correction step type (#2747)
  17. ENCD-4493 Limit RIN audit to certain assays (#2743)
  18. ENCD-4593 add histone and control chip-seq titles (#2741)
  19. ENCD-4504 miRNA audits (#2736)
  20. ENCD-4503 micro RNA qc (#2679)
  21. ENCD-4570 Add M21 V29 V30 genome annotations (#2745)
  22. ENCD-4544 deleted the file atacseq qm json file (#2738)
  23. ENCD-3108 Add new target categories (#2742)
  24. SNO-88 fix-user-search-count (#2722)
  25. ENCD-4589 Add an experimental audit for biosample characterization. (#2739)
  26. ENCD-4316 Make generic matrix-rendering component. (#2728)
  27. ENCD-4575 software-column-used-by (#2737)
  28. ENCD-4545 Update visualization browser list (#2730)
  29. ENCD-4597 show-all-datasets (#2733)

84.0 (released) snovault 1.0.28

  1. ENCD-4591 add-title-column-back (#2723)
  2. ENCD-4590 fix-facet-num-line (#2725)
  3. ENCD-4592 Update to Java 9 in travis (#2724)
  4. ENCD-4585 Update to snovault 1.0.28 (#2721)
  5. SNO-89 Fix backoff error key in indexer (#2720)
  6. ENCD-4559 x-limit-zero-results (#2711)
  7. ENCD-4349 restrict gm reagents (#2672)
  8. ENCD-4578 Fix s3 to s3 allow flag in deployment (#2708)
  9. ENCD-4243 Make dataset biosample boost values consistent (#2712)
  10. ENCD-4527 walkme-production-snippet (#2690)
  11. ENCD-4581 Temp install java 8 through aws (#2718)
  12. ENCD-4577 Add documents on characterization page (#2716)
  13. ENCD-4565 remove back slashes from search terms (#2714)
  14. ENCD-4576 Change header links and add FAQ script (#2715)
  15. ENCD-4556 Remove lane reqs for massspec characs (#2700)
  16. ENCD-4311 href-column-is-blank (#2713)
  17. SNO-85 facet-reappearing (#2676)
  18. ENCD-4506 make fragmentation method a list (#2683)
  19. ENCD-4542 Display biosample table on GM pages (#2699)
  20. ENCD-4407 update the columns and facet titles
  21. ENCD-4548 fix fallback images on collection pages (#2703)
  22. ENCD-4560 update typeaheads after selections (#2702)
  23. ENCD-4497 get rid of duplicate columns using titles
  24. ENCD-4564 add target typeahead to AntibodyLot pages (#2707)
  25. ENCD-4412 Add Clear Cart item to cart menu (#2695)
  26. ENCD-4554 fix-annotation-url (#2697)

83.0 (released) / snovault 1.0.27

  1. ENCD-4569 Update snovault to 1.0.27 (#2704)
  2. ENCD-4562 Setup s3tos3 copy on test (#2698)
  3. ENCD-4555 Fix key errors in vis indexing (#2696)
  4. ENCD-4543 fix-status-hierarchy (#2677)
  5. ENCD-4550 Fix deploy console output (#2691)
  6. ENCD-4170 exclude-restricted-files (#2670)
  7. ENCD-4510 Fix human donor children calc prop (#2684)
  8. ENCD-4513 add collections links to menu (#2681)
  9. ENCD-3919 index-vis-blobs-on-deploy (#2685)
  10. ENCD-4517 Add new property introduced_elements to user interface (#2671)
  11. SNO-83 rotate jpg and tiff attachment based on EXIF (#2667)
  12. ENCD-3952 add new assay category, mpra, update ontology.json
  13. ENCD-4347 add efo derives from capability, remove unnecessary slimming
  14. ENCD-4384 Update assay name ISO-seq to long read RNA-seq
  15. ENCD-4489 add imputation annotation_type (#2654)
  16. ENCD-4414 Allow users to add exp to carts from series (#2665)
  17. ENCD-4507 Handle long cart operations (#2661)
  18. ENCD-4494 remove-duplicate-embedding (#2659)
  19. ENCD-4521 add-insert-user-meenakshi (#2653)
  20. ENCD-4469 Add stimulation to treatment type (#2646)
  21. ENCD-3422 datasets-table-publication (#2660)
  22. ENCD-4524 update audit matrix (#2662)
  23. ENCD-4526 Change date format for Pages (#2663)
  24. ENCD-4477 added-changelogs (#2668)
  25. ENCD-4530 Fix duplicate alternate accessions (#2669)
  26. ENCD-4464 add GM category enums (#2634)
  27. ENCD-4523 Fix ENSEMBL visualization (#2645)

82.0 (released) / snovault 1.0.26

  1. ENCD-4509 Add test back (#2640)
  2. ENCD-4518 Fix javascript error for sorting dates (#2642)
  3. ENCD-4481 Update to snovault 1.0.26 (#2639)
  4. ENCD-4500 remove-uploading-private-status-list (#2636)
  5. ENCD-3901 Support multiple carts per user (#2614)
  6. ENCD-4487 reset-upload-bucket (#2635)
  7. ENCD-4505 fix-file-bucket-audit (#2638)
  8. ENCD-4482 adding lane to characterizations review (#2624)
  9. ENCD-4483 Cleanup deploy output and short aws name(#2626)
  10. ENCD-4353 Refactor-out-matrix-and-result (#2539)
  11. SNO-80 Typeahead for facets (#2632)
  12. ENCD-3877 annotation-download-btn
  13. ENCD-4474 model restriction map (#2617)
  14. ENCD-4473 add-MPRA-assay (#2623)
  15. ENCD-4418 Add ontology dbxrefs to biosample page (#2637)
  16. ENCD-4305 Turn Superseded by into links on exp file pages (#2633)
  17. ENCD-4457 organoid age (#2631)
  18. ENCD-4485 bug report camel case (#2629)
  19. ENCD-4467 Numerical facets sorted by value not frequency (#2628)
  20. ENCD-3877 annotation-download-btn
  21. ENCD-4449 use top level class files property for Annotation
  22. ENCD-4401 remove-approvalrequired (#2616)
  23. ENCD-4217 Rendering error series objects (#2627)
  24. ENCD-4484 Allow deployment set ssh id file (#2625)
  25. ENCD-4348 Restrict ontologies for in vitro diff cells (#2620)
  26. ENCD-4476 add-spaces-schema (#2615)
  27. SNO-73 Add uuid queue module
  28. ENCD-4456 Override update objs in vis reg indexers
  29. ENCD-4450 add two sources to alias namespace (#2618)
  30. ENCD-4475 Fix pub priv bucket variables (#2613)

81.0 (released) / snovault 1.0.25

  1. ENCD-4462 fixing the AB characterization view bug (#2606)
  2. ENCD-4463 embed BiosampleType in antibody characterization (#2603)
  3. ENCD-4460 Update AnalysisStep changelog (#2605)
  4. ENCD-4461 Revert libraries for exp type matrix (#2602)
  5. ENCD-4429 Lower audit severity for missing reagents in GM (#2601)
  6. ENCD-4458 Update snovault 1.0.25 (#2600)
  7. ENCD-4240 Allow review characterizations (#2591)
  8. ENCD-4425 Update audits exp and genetic mod targets (#2598)
  9. ENCD-4445 Handle login for related files in file tables. (#2597)
  10. ENCD-4455 Notify indexer for file update bucket (#2599)
  11. ENCD-4453 Add idx file format (#2594)
  12. ENCD-4427 file-bucket-audit (#2580)
  13. ENCD-4298 Ontology update colon and PLAC-seq (#2590)
  14. ENCD-4251 Combine reorganize technical replicates (#2567)
  15. ENCD-4431 Change report file download name (#2571)
  16. ENCD-4444 Highlight selected facet terms numbers (#2587)
  17. ENCD-4408 mobile menu readability (#2593)
  18. ENCD-4420 Remove biosample type name id props (#2585)
  19. ENCD-4014 library restriction enzyme audit (#2537)
  20. ENCD-4419 use biosample ontology for audit (#2589)
  21. ENCD-4435 Add ENCv5 ccre internal_tags to datasets (#2588)
  22. ENCD-4406 exclude fly RNAi from reagents audit (#2570)
  23. ENCD-4227 add-PLAC-seq-to-assays (#2584)
  24. ENCD-4405 Add enrichment to analysis step types enum (#2582)
  25. ENCD-4416 Revise audit_inherit list of AntibodyLots (#2583)
  26. ENCD-4402 Add Jennifer Z to submitters (#2572)
  27. ENCD-4397 introducing GM in metadata tsv (#2557)
  28. ENCD-4439 add PLAC-seq in generate-ontology (also #2590)

80.0 (released) / snovault 1.0.24

  1. ENCD-4423 Update dalliance to version 1.0 (#2566)
  2. ENCD-4417 Update to snovault 1.0.24 (#2563)
  3. ENCD-3971 Update node npm to version 10 (#2553)
  4. ENCD-4359 Fix recursive is_part_of audit function (#2552)
  5. ENCD-4325 Juicebox browser (#2554)
  6. ENCD-4360 connect biosample type (#2560)
  7. ENCD-4396 Citation note (#2555)
  8. ENCD-4388 excluding not relevant experiments form RE audits (#2551)
  9. ENCD-4355 add introduced gene link (#2559)
  10. ENCD-4375 Restore SRA dbxrefs linkouts (#2558)
  11. ENCD-4393 add-gene-alignments (#2556)
  12. ENCD-4369 Install redis server (#2543)
  13. ENCD-4377 Add Ubiquitination to target mod enum (#2550)
  14. ENCD-4399 fix-linux-travis-option (#2547)

79.0 (released) / snovault 1.0.22-23

  1. ENCD-4340 get-or-create-carts-with-types (#2541)
  2. ENCD-4372 Update to snovault 1.0.23 (#2546)
  3. ENCD-4367 Update simple for queue module (#2542)
  4. ENCD-4371 Update to snovault 1.0.22 (#2544)
  5. ENCD-4335 Remove npm shrinkwrap again (#2540)
  6. ENCD-4312 genetic modification audit (#2528)
  7. ENCD-3665 add file format dependency (#2523)
  8. ENCD-4333 Add release candidate options to deploy (#2503)
  9. ENCD-4323 Promote released objects (#2535)
  10. ENCD-4346 Added new output type for HiC files (#2531)
  11. ENCD-4334 Added status facet to Matrix view on y axis (#2520)
  12. ENCD-4299 Fix anti body lot target_organisms (#2529)
  13. ENCD-4358 add cell-free sample BiosampleType (#2536)
  14. ENCD-4306 remove-improper-styling (#2524)
  15. ENCD-4338 Allow repo to be specified on deploy (#2509)
  16. ENCD-4327 changed audit level for missing step run (#2513)
  17. ENCD-4201 Add Jen to test data insert (#2518)
  18. ENCD-4328 disable-btn-unavail-files (#2521)
  19. ENCD-4218 fix biodalliance visualize multiple datasets (#2522)
  20. ENCD-4315 cleanup-mutated-gene (#2526)
  21. ENCD-4273 Inconsistent antibody handling (#2530)
  22. ENCD-4319 improve BiosampleType (#2516)
  23. ENCD-4308 fix-audit-clear-filter (#2499)
  24. ENCD-4324 Added-min-width-to-y-axis-label (#2506)
  25. ENCD-4265 matrix-audit-text-update (#2507)
  26. ENCD-4250 Make target synthetic organism as tag (#2510)
  27. ENCD-4272 no-add-treatments (#2514)
  28. ENCD-4326 Fix HTML entities for quotes (#2511)
  29. ENCD-4297 Fix back button behavior and page jumping (#2515)
  30. ENCD-3855 Filter ReEpig by assay facet by title (#2517)

78.0 (released) / snovault 1.0.21

  1. ENCD-4332 Update to snovault 1.0.21 (#2502)
  2. ENCD-4301 Refactor index UUID server (#2485)
  3. ENCD-4263 Only show released quality metrics (#2450)
  4. ENCD-4195 Update ontology with mintchip slims (#2500)
  5. ENCD-4321 Fix import of ExperimentTable (#2498)
  6. ENCD-4317 Update snovault to 1.0.20 (#2494)
  7. ENCD-4205 biosample type (#2442)
  8. ENCD-4245 skip-restricted-acl (#2490)
  9. ENCD-4279 Biosample preservation (#2493)
  10. ENCD-4033 Search page type-specific header (Req SNO-66) (#2492)
  11. ENCD-4281 fix-audit-text-message (#2465)
  12. ENCD-4223 Make internal_tags badges clickable to search pages (#2467)
  13. ENCD-4289 Update genetic modification tags metadata (#2491)
  14. ENCD-4244 audit-error-page (#2461)
  15. ENCD-4271 fix-treatment-tem-id-regex (#2475)
  16. ENCD-4231 matched set controls (#2474)
  17. ENCD-4295 fix target title in JSON (#2486)
  18. ENCD-4291 changed modification_type to category in gm schema (#2478)
  19. ENCD-4252 disable-download-restricted-files-admin (#2481)
  20. ENCD-4300 Remove checkfiles folder (#2484)
  21. ENCD-4288 Update requests to 2.20.0 (#2483)
  22. ENCD-4195 ontology update sept18 (#2489)
  23. ENCD-4267 Remove redirect from apache config (#2459)
  24. ENCD-4142 Update calc prop assembly on dataset (#2437)
  25. ENCD-4255 fix-biosample-audit-bug (#2470)
  26. ENCD-4282 Add PGP internal_tags badge (#2468)
  27. ENCD-4256 Fix region search back button functionality (#2463)
  28. ENCD-4280 Remove table margin (#2462)
  29. ENCD-4239 Add biosample to query string on matrix (#2460)
  30. ENCD-4199 Ignore npm shrinkwrap (#2477)

77.1 (released) / 3998 Bug Fix

  1. ENCD-3998 Target upgrade to return gene uuid (#2466)

77.0 (released) / snovault 1.0.19

  1. ENCD-4237 bdd-test-for-search (#2435)
  2. ENCD-4274 Update to snovault 1.0.19 (#2446)
  3. ENCD-3159 Initial shopping cart (#2430)
  4. ENCD-4209 Add index flags to indexers and fix logs (#2402)
  5. ENCD-4000 represent histone modification in Target (#2416)
  6. ENCD-3998 Link target to gene and link gene from targets. (#2416)
  7. ENCD-4229 Fix no story news news crash (#2445)
  8. ENCD-3701 Update events from search page text box (#2428)
  9. ENCD-4185 s3-public-url (#2425)
  10. ENCD-4257 Revert copy to deepcopy for matrix factory(#2439)
  11. ENCD-4220 Remove references to release ready status (#2436)
  12. ENCD-4176 fix BDSC links (#2434)
  13. ENCD-4254 Raise file validation error audit level in exp (#2433)

76.0 (released) / snovault 1.0.18

  1. ENCD-3926 Refactor search related views (#2422) (#2424)
  2. ENCD-4202 fixing missing control audit (#2398)
  3. ENCD-4197 Red audit for missing step_run (#2397)
  4. ENCD-4221 Fix button styles (#2414)
  5. ENCD-4207 Added emma to user file (#2403)
  6. ENCD-4177 Adding btn to convert page to JSON (#2411)
  7. ENCD-3830 Make text area fields in forms (#2405)
  8. ENCD-4206 calc prop rebased (#2418)
  9. ENCD-4190 no-hypen-on-experiment-values (#2399)
  10. ENCD-4200 show-facebook-share-btn (#2401)
  11. ENCD-4196 Reduce cloud init size (#2392)
  12. ENCD-4208 Add png addition to qc mime types (#2400)
  13. ENCD-4216 Add RefSeq to dbxrefs in gene schema (#2410)
  14. ENCD-4173 Add Paul to test user inserts (#2404)
  15. ENCD-4171 Reset default audit inherit (#2393)

75.1 (released)

  1. ENCD-4214 Update to snovault 1.0.17 (#2406)

75.0 (released)

  1. ENCD-4204 Update to snovault 1.0.16 (#2394)
  2. ENCD-4193 block-on-orange-audit (#2390)
  3. ENCD-4153 alter-select-distinct-values (#2389)
  4. ENCD-4135 integrity-num (#2375)
  5. ENCD-4188 add khine to testdata (#2391)
  6. ENCD-4187 fix ENSEMBL links for mouse. (#2380)
  7. ENCD-4160 Added Casey, Jason, and Zack to users (#2371)
  8. ENCD-4159 adjusting GM characterization audit (#2366)
  9. ENCD-4038 Adding matrix bdd tests (#2335)
  10. ENCD-4182 Patch dbxref pattern in Gene. (#23
  11. ENCD-4166 RIN internal action audit (#2365)

74.0 (released)

  1. ENCD-4169 Update to snovault 1.0.15
  2. ENCD-4131 set-status-endpoint (#2363)
  3. ENCD-4168 add-embed-cache-to-ini (#2367)
  4. ENCD-4167 Explicitly set availability zone in deploy script (#2361)
  5. ENCD-4163 Update to snovault 1.0.14 (#2360)
  6. ENCD-3997 Create Gene object (#2307)
  7. ENCD-4083 Allow aws s3 to s3 file transfer (#2358)
  8. ENCD-4162 update snovault 1.0.13 (#2359)
  9. ENCD-4136 Add dry run arg for deployment (#2357)
  10. ENCD-4123 audit chip (#2343)
  11. ENCD-4154 Remove unused search type arg (#2355)
  12. ENCD-4141 Add alias namespaces (#2344)
  13. ENCD-4152 Make organism scientific_name required (#2354)
  14. ENCD-4107 Added experiment_class to experiment schema (#2330)
  15. ENCD-4134 add RIN number property to Library (#2348)
  16. ENCD-3732 replicate-sorting (#2329)
  17. ENCD-4146 Restore FileDownloadButton constructor (#2352)
  18. ENCD-4149 Allow bin test log arg for workbook loading (#2351)
  19. ENCD-4144 Fix failing impersonation test button size (#2350)
  20. ENCD-4118 set minimum value to 0 for ch coordinates in GM (#2347)
  21. ENCD-4143 Add asserts to status trigger tests

73.0 (released)

  1. ENCD-4129 update-to-snovault-1.0.12 (#2336)
  2. ENCD-4064 release-endpoint (#2281)
  3. ENCD-4017 Fulfill ECP requests for home page additions. (#2326)
  4. ENCD-4105 Add DGGR dbxref processing (#2325)
  5. ENCD-4108 audit matched (#2324)
  6. ENCD-4089 Deactivated-rep-num-in-annot-table (#2315)
  7. ENCD-4074 toolip-overlay (#2313)
  8. ENCD-4102 changed audit from WARNING to ERROR (#2327)
  9. ENCD-3903 add documentation for schema page (#2332)
  10. ENCD-3563 updated sc replication audit (#2322)
  11. ENCD-4087 fixed-flybase-search (#2312)
  12. ENCD-4051 Change schemas to set minimum int values (#2309)

72.0 (released)

  1. ENCD-4103 Fix tests broken by SNO-41 (#2317)
  2. ENCD-4098 Update to snovault 1.0.11 (#2314)
  3. ENCD-4072 Remove es master from deployment (#2302)
  4. ENCD-4086 Analysis-Step schema (#2305)
  5. ENCD-4048 rep-num-in-pub-n-exp (#2311)
  6. ENCD-4093 Fix initial region indexing failure (#2308)
  7. ENCD-3728 Fix build error (#2306)
  8. ENCD-4020 Allowing specification of Sets as controls (#2296)
  9. ENCD-4055 removed-some-styling-on-raw-data (#2277)
  10. ENCD-4057 properly-format-data-on-biosample-page (#2276)
  11. ENCD-4088 Remove extra code added in ENCD-3306 (#2310)
  12. ENCD-4040 vis index replicate conditional (#2294)
  13. ENCD-3718 return-404-when-file-not-found (#2278)
  14. ENCD-4073 Revert accidental blocked dataset status expansion (#2291)
  15. ENCD-4077 Fix deploy volume size type (#2304)
  16. ENCD-3776 move-to-standard-status (#2295)
  17. ENCD-4078 Remove unused statuses (#2293)
  18. ENCD-4058 expanding-matrix-creates-unaligned-header (#2280)
  19. ENCD-4085 Add weiwei as a submitter (#2298)
  20. ENCD-4081 Add Yunhai as a submitter in local test. (#2288)

71.0 (released)

01. ENCD-4046 update to snovault 1.0.10, add CHANGES (#2275) 02. ENCD-3306-fix-line-in-table (#2271) 03. ENCD-4045 gdpr auth0 (#2274) 04. ENCD-3695-upgrade-to-boto3 (#2272) 05. ENCD-3883-add-pmi-data (#2263) 06. ENCD-3727 added hypen for long words (#2270) 07. Add zoldello (Phil) as an authorized submitter for the test environments. ENCD-4049 08. ENCD-4019 adding readname_details field to the file.json (#2260) 09. ENCD-4042 Update genetic mods for functional characterization experiments (#2262) 10. ENCD-3629 Refactor and redesign status displays. (#2246) 11. ENCD-4034 SVG tooltip and minor JS clean up (#2255) 12. ENCD-3911 Added a break above document box (#2256) 13. ENCD-3364 fixed text and link button misalignment (#2257)

70.0 (released)

01. ENCD-4037 Update snovault 1.0.9 (#2258) 02. ENCD-4029 Update to snovault 1.0.8 (#2254) 03. ENCD-3889 supersedes refepi (#2247) 04. ENCD-3871-target-standard-status (#2252) 05. ENCD-4011 Fix wrong vars in buildout candidate config file (#2241) 06. ENCD-3867 Display proper replicate_type string (#2249) 07. ENCD-4015 adding an audit for read_count and test for it (#2242) 08. ENCD-4010 fixing a typo in the samtools flagstat quality metric (#2238) 09. ENCD-3995 Update file output_type (#2239) 10. ENCD-4016 adding community to users (#2243) 11. ENCD-3957 Add biosample accession to report columns (#2250) 12. ENCD-3970 Add encore badge (#2251) 13. ENCD-4008-fix-source-title (#2253) 14. ENCD-4007-nginx-proxy-header (#2244) 15. ENCD-3981 remove histone modification (#2240) 16. ENCD-3963 Remove antibody accession column (#2233) 17. ENCD-3974 Update biosample organoid (#2234) 18. ENCD-3641 fix navigate to file download URI (#2237)

69.0 (released)

01. REG-9 Fix vis button for region search (#2210) 02. ENCD-3986 Update to snovault 1.0.7 (#2229) 03. ENCD-3950 Require date_submitted in submitted experiments (#2224) 04. ENCD-3923 Allow es to deploy separately from encoded 05. ENCD-3620 Update deploy options for region search 06. ENCD-3621 Refactor deploy script 07. ENCD-3980 Organize ini files and vars 08. ENCD-3216 Hide antibody characterizations via user access level (#2225) 09. ENCD-3726 adding platform to library (#2223) 10. ENCD-3959 Add int and bool to displayed QC types (#2212) 11. ENCD-3973 Redo how GM characterization documents get displayed (#2219) 12. ENCD-3979 Fix zc buildout for pypi update (#2221) 13. ENCD-3961 eslint AirBnB npm package updates (#2214)

68.0 (released)

01. ENCD-3965 Update to snovault 1.0.6 (#2209) 02. ENCD-3934 fix plate location in library (#2208) 03. ENCD-3944 Add organ slim shims & update ontology.json (#2201) 04. ENCD-3934 Update to original 3934 commit (#2207) 05. ENCD-3739 rewriting chip control read depth audit (#2188) 06. ENCD-3775-started-to-in-progress (#2202) 07. ENCD-3451 Summary page (#2200) 08. ENCD-2992 Remove unused status (#2206) 09. ENCD-3960 Fix batch download lookup column test (#2205) 10. ENCD-3935 adding new biosample type "single cell" (#2193) 11. ENCD-3898 adding an audit flagging "tagging" GM without characterization (#2187) 12. ENCD-3886 Update deploy machine instance types (#2181) 13. ENCD-3863 Eliminate repeated values in report TSV (#2136) 14. ENCD-3938 Adding new Series type "AggregateSeries" (#2190) 15. ENCD-3934 adding "barcode_details" to library schema (#2197) 16. ENCD-3189 Traverse root using external_accession key from files (#2178) 17. ENCD-3645 & ENCD-3716 Strip white spaces from values (#2194) 18. ENCD-3716 Strip white spaces from values (#2194) 19. ENCD-3773-pipeline-status (#2189) 20. ENCD-3870-publication-status-mixin (#2191) 21. ENCD-3780-remove-ready-for-review (#2192) 22. ENCD-3772-remove-virtual (#2195) 23. ENCD-1 Add treatments amount, duration to metadata.tsv 24. ENCD-2845 Quick fix for biosamples with both the sexes 25. ENCD-3868 - Adding unit tests for batch_download helpers 26. ENCD-3823 & ENCD-3864 - Filter out restricted files and refactor batch_download 27. ENCD-3864 - Filter out restricted files and refactor batch_download

67.1 (released)

  1. ENCD-3916 Fix for broken metadata queries (#2179)

67.0 (released)

01. ENCD-3915 Remove chromedriver lock from Travis (#2174) 02. ENCD-3892 Update to snovault 1.0.5 (#2173) 03. ENCD-3809 Add run_types for pacbio and oxford nanopore (#2172) 04. ENCD-3839 Remove schemas for the deleted objects (#2167) 05. ENCD-3891 Fix file test for duplicates in derived_from (#2162) 06. ENCD-3908 Update indexer doc for march 2018 update 07. ENCD-3913 Update regionsearch MAX_CLAUSES request_timeout 08. ENCD-3900 Increase demo volume size 09. ENCD-3756 Remove scorefilter in dnase visuals 10. ENCD-3907 Adopting UCSC bigNarrowPeak type 11. ENCD-3260 Refactor visualization 12. ENCD-3602 Migrate indexers to region and secondary 13. ENCD-3894 Move NIH cert audit to experiment (#2166) 14. ENCD-3840 Add link to linkFrom linkTo schema properties (#2168) 15. ENCD-3899 Fix exp audit trigger on non-encode pipelines (#2170) 16. ENCD-3604 Update boost to include GM accessions (#2171) 17. ENCD-3848 Remove immortalize from cell line (#2164) 18. ENCD-3854 Fix report description column sort error (#2150) 19. ENCD-3893 Add NIH cert to biosample facets (#2165) 20. ENCD-3828 Update redacted alignments (#2163) 21. ENCD-3841 Add collapsing sections on schema pages (#2154) 22. ENCD-3880 Add Alembic documentation (#2152) 23. ENCD-3821 Show biosample characterization doc links (#2145) 24. ENCD-3882 Update DOI preferred resolver url (#2135) 25. ENCD-3879 Pin Alembic version (#2151)

66.0 (released)

01. ENCD-3878 Update to snovault version 1.0.4 (#2148) 02. ENCD-3834 Add Alembic framework for Postgres migrations (#2142) 03. ENCD-3869 Downgrade chromedriver version 2.33 (#2143) 04. ENCD-3827 Fix ES5 version in README (#2141) 05. ENCD-3698 Add Institutional certifications to biosample (#2140) 06. ENCD-1934 Format schema displays (#2115) 07. ENCD-3865 Update to snovault version 1.0.3 (#2139) 08. ENCD-3836 Small heap single machine (#2137) 09. ENCD-3819 Add biosample preservation method (#2122) 10. ENCD-3835 Fix inconsistent platforms audit HiSeq2K 2.5K (#2133) 11. ENCD-3341 Add new output_types to file json (#2132) 12. ENCD-3853 Remove UCSC logos (#2134) 13. ENCD-3757 Adjust histone broad peak read depth audit (#2125) 14. ENCD-3831 Add exp audit to flag standards violations (#2124) 15. ENCD-3766 Add submitter comments to certain js pages (#2123) 16. ENCD-3820 Biosample: PMI property (#2120) 17. ENCD-3798 Ontology Update Jan2018 (#2119) 18. ENCD-3816 Update selenium version to 3.8.1 (#2118) 19. ENCD-3803 Allow fastq_sig to accept 3 in SRR headers (#2113) 20. ENCD-3456 Stringify array and object items in a cell (#2111) 21. ENCD-3762 Add RegulomeDB internal_tag and badge (#2110) 22. ENCD-3421 Properly link home chart to matrix (#2108) 23. ENCD-2567 New report page column selector modal (#2105)

65.3 (released)

  • ENCD-3851 Add max clause es5 updates

65.2 (unreleased)

  • Update to snovault 1.0.2 (#2128) -> ENCD-3845

65.1 (unreleased)

  • ENCD-3813 Update to snovault 1.0.1 (#2116)

65.0 (unreleased)

  1. ENCD-3815 Fix tests for facet aggregation set to 200 (#2109)
  2. ENCD-3795 Fix spelling in histone and idr qm jsons (#2104)
  3. ENCD-3810 Set facet aggregation to 200 in search (#2107)
  4. ENCD 3749 Update README for ES5 and dependency requirements (#2087)
  5. ENCD-3741 Search for objects based on associated grant number (#2103)
  6. ENCD-3792 Add histone_chip_quality_metric PIP-198 (#2101)
  7. Update to snovault v1.0.0 -> ENCD-3788
  8. ENCD-3745 Add platform to file and exp facets (#2088)
  9. ENCD-3765 Set max_result_window for annotations index (#2083)
  10. ENCD-2488 ES5 Update aka RM3910
  11. ENCD-3546 Create 'save and add' button to add forms (#2100)
  12. ENCD-3700 Remove unreplicated exp audit for genetic mod DNase (#2096)
  13. ENCD-3781 Resolve WGBS lambda audit error (#2095)
  14. ENCD 3759 Fix WGBS coverage audit (#2093)
  15. ENCD-3743 Fix read depth audits for DNase and ChIP (#2091)
  16. ENCD-3760 Remove the NTR assay audit (#2089)
  17. ENCD-3724 Adjust facet term display check (#2086)
  18. ENCD-3755 Remove schemas for RNAi and construct characterizations (#2085)
  19. ENCD-3737 Add M14 gencode annotations to file enums (#2084)
  20. ENCD-3708 Update publication states (#2077)
  21. ENCD-3699 Remove mixed run type audit from DNase (#2065)
  22. ENCD-3661 Update drawing file graphs and JS Tests (#2080)
  23. ENCD-3764 Fix message typo in Assay audit (#2081)
  24. ENCD-3473 Fix for unknown error in batch_download
  25. ENCD-3579 Fix for batch download error
  26. ENCD-3566 Fix JS FileInput add document (#2076)
  27. ENCD-3597 Use obj picker for user impersonation (#2068)
  28. ENCD-3721 Allow 'in vitro sample' to have biosample_term_name (#2067)
  29. ENCD-3734 file audit escalation (#2066)

0.1 (unreleased)